Input Files format

1. Reference file

Reference file is needed in the scan module, and the version and contig name of reference you used should be in accordance with your bam files. And the reference should be save as uncompressed fasta (fa) format.

2. microsatellite file

Microsatellite file is need in all module of MSIsesnsor-pro,it contain the chromosome, location, repeat unit, repeat unit length, and other information of each microsatellite.

Example:

chromosome	location	repeat_unit_length	repeat_unit_binary	repeat_times	left_flank_binary	right_flank_binary	repeat_unit_bases	left_flank_bases	right_flank_bases	threshold	supportSamples
chr1	3780974	1	0	11	221	321	A	ATCTC	CCAAC	0.080981	30
chr1	3784993	1	0	13	885	758	A	TCTCC	GTTCG	0.007576	18
chr1	3836468	1	3	24	342	80	T	CCCCG	ACCAA	0.061750	19
chr1	3872414	1	0	13	834	545	A	TCAAG	GAGAC	0.02842	28
chr1	4712522	3	20	7	662	421	CCA	GGCCG	CGGCC	0.024391	3

Note:

1. Columns with *_binary means: binary conversion of DNA bases based on A=00, C=01, G=10, and T=11.
2. threshold means: the unstable baseline of slippages. It is calculated in baseline module and applied in pro module.
3. supportSamples means: the number of samples with sufficient reads covered.

3. bam file

bam file need to be sorted and the index file are required.

4. configure file of baseline module

configure file is needed in baseline module, the first column is the sample name and the second is the absolute path of its bam file.

Example:

case1   /path/to/normal/case1_sorted.bam
case2   /path/to/normal/case2_sorted.bam
case3   /path/to/normal/case3_sorted.bam